[gmx-users] Query

[Priya Das]

Yes Justin...i watched the dynamic structure carefully. As it is a
transmembrane protein it is stringently moving.
The dynamic movement of the structure seems fine.
I used the backbone of protein for calculating Rmsd.
I also want to know the ligand stability, for it i need to check the least
square fit of ligand , right?
On May 19, 2015 5:11 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 5/19/15 6:29 AM, Priya Das wrote:
>
>> Dear all,
>>
>> While generating RMSD plots of protein in presence of ligand, i am getting
>> a RMSD of around 4.5 Angstrom around 10 ns after which the system is
>> almost
>> stable.
>> Is it an acceptable RMSD?
>> What is the acceptable range for RMSD for structures?
>>
>>
> There is no general rule, and a number without context is meaningless.
> How did you calculate the RMSD - backbone? heavy atoms? all atoms?  Does
> your protein have a lot of variable loops, and did you consider these?  Or
> did you just consider structured parts of the protein?  Did you include
> termini?  Did you watch the trajectory to see what's happening?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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